From 3676e8d73e89f0f63b18c3d42232cd780344d452 Mon Sep 17 00:00:00 2001
From: Ally Hawkins The PanglaoDB cell types seem to be more specific than the ones
present in Blueprint Encode, similar to the observation with neurons. We
-should keep epithelial cell.Summary of cell type ontologies in
reference files
Ally Hawkins
-2024-12-17
+2024-12-18
@@ -512,7 +512,7 @@ Setup
panglao_annotation = "human_readable_value"
)
-## Rows: 178 Columns: 3
-## ── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
+## ── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (3): ontology_id, human_readable_value, panglao_cell_type
##
@@ -693,8 +693,8 @@
Latest common ancestor (LCA) between PanglaoDB and Blueprint
dplyr::mutate(lca = dplyr::if_else(blueprint_ontology == panglao_ontology, blueprint_ontology, lca)) |>
# join in information for each of the lca terms including name, number of ancestors and descendants
dplyr::left_join(cl_df, by = c("lca" = "cl_ontology"))
+## Warning: Expected 3 pieces. Missing pieces filled with `NA` in 7967 rows [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
-## 20, ...].
## Warning: Expected 3 pieces. Missing pieces filled with `NA` in 7967 rows [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
+## 18, 19, 20, ...].
Distribution of ancestors and descendants
ggplot(lca_df, aes(x = total_ancestors)) +
@@ -1733,7 +1733,7 @@
Myeloid leukocyte
then I would argue we shouldn’t keep myeloid leukocyte. Noting that
after discussion we have decided to keep this one since T and B cells
are much easier to differentiate based on gene expression alone than
-cells that are party of the myeloid lineage.
+cells that are part of the myeloid lineage.
Progenitor cell
@@ -3347,7 +3347,9 @@ Epithelial cell
Epithelial cells
but not when it is
+Keratinocytes
.
## [1] "blood cell" "hematopoietic precursor cell" "lining cell" "perivascular cell"
-## [5] "supporting cell"
+## [1] "blood cell" "hematopoietic precursor cell" "lining cell"
+## [4] "perivascular cell" "supporting cell"
It looks like I am losing a few terms I already said were not specific and then a few other terms, like “hematopoietic precursor cell” and “perivascular cell”. I’ll look at both of those to confirm we would @@ -3909,9 +3911,12 @@
neuron
and
+neuron
and
epithelial cell
even though they do not pass the threshold
-for number of descendants.epithelial cell
should
+only be included if the Blueprint Encode name is
+Epithelial cells
and not
+Keratinocytes
.
lining cell
, blood cell
,
progenitor cell
, bone cell
, and